Plot hole: Just after you finish defeating The Jumbo Shrimp, SpongeBob is back at Squidward's house telling him the story. Squidward tells SpongeBob that something is wrong with Gary and SpongeBob goes back over to the house to see what is wrong with him. SpongeBob finds out that Gary is hungry and attempts to go to Patrick to see what to get because they are out of pet food. This makes no sense because in level one earlier, SpongeBob opened up a pantry filled with pet food. There's no way they could have been out of food.
Plot hole: After finishing the mission to defeat The Dirty Bubble atop the Sea Needle, the game completes, the Dirty Bubble is stopped and Bikini Bottom is saved from the little dirty bubbles infecting them. After saving the day, the game lets you go back to Bikini Bottom to finish off some other missions, but despite this the citizens are still infected by the little dirty bubbles and if you go back to the Sea Needle, the Dirty Bubble is still waiting there and reading to be battled again.
Continuity mistake: The Salty Spitoon, Weenie Hut Jr's and Super Weenie Hut Jr's are depicted as in the Bikini Bottom: Restaurant District near The Chum Bucket and The Krusty Krab. In the SpongeBob episode that shows the three clubs (No Weenies Allowed), the clubs were near Goo Lagoon. This distances between the three clubs has also changed.
Bug: Walk through the higher ground parts of the Bikini Bottom: Restaurant District. The higher ground parts are between the exit to Downtown Bikini Bottom and the exit to Boating School Test Course. On the fifth part of the higher ground, there will a zombie who will be seen with one of his feet OVER the edge of the higher ground. This zombie and SpongeBob are still able to walk totally fine despite this.
Continuity mistake: Level Two: There is a Scary Glow In The Dark Beard and Mustache in SpongeBob's House: Upstairs. This was never visible in SpongeBob's House: Upstairs in Level One and there was no time for SpongeBob to put it there because he was saving the town from the little Dirty Bubbles.
Continuity mistake: Level Two: You start in level two in SpongeBob's House: Upstairs. Walk over to the light switch and turn off the light. In the "Use the Light Switch" pic, see how there is nothing next to the bed (except for the clock). However, as soon as you turn off the "Use the Light Switch" pic, a Scary Glow In The Dark Beard and Mustache instantly appears out of nowhere.
Bug: Level One: Approach Goo Lagoon Pier in Goo Lagoon to confront Man Ray. If you approach from the left after down jumping from a higher ground, notice the first half of the pier is completely empty and Scooter is seen standing on the next corner. Then as you continue to walk towards the pier, a zombie guy miraculously appears in shot.
Other mistake: There are codes on the Chum Bucket menu. These codes are used to put in the order machine. If you put the codes in the order machine, only a Chum Burger will be ordered. If you put in a code for Chum Fries, Chum Shake or Chum on a Stick, it won't be ordered even though you put in the specific code. All that will happen is four question marks pop up.
Bug: This glitch is pretty cool. When you use the Super Strength to pick up a box, take it to the nearest wall or higher ground level (before jumping). Now get as close as you can to the wall or higher ground level and instantly cancel you're super power. The box will fade through you. Then push jump a couple of times and when you come out of the box you start to jump through the air as if you were triple jumping.